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Fix differential equation tutorial #296

Merged
merged 7 commits into from
May 2, 2022
Merged

Fix differential equation tutorial #296

merged 7 commits into from
May 2, 2022

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devmotion
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@devmotion devmotion commented Apr 26, 2022

I've wanted to do this for quite some time but unfortunately my computer broke while working on an update...

So here are some fixes for the differential equation tutorial.

Most notably,

  • it fixes the MvNormal deprecations
  • fixes the trajectories of posterior samples (the used the wrong parameters)
  • it uses more "modern" and simpler SciML syntax
  • specifies the solver for the DDE example correctly.

Preview: https://julialang-buildkite-artifacts.s3.amazonaws.com/turingtutorials/e3c8bc002f5223b50eb6e9c7902473c040159c0aa4d5942d979166fa05bcb422/html/10-bayesian-differential-equations/10_bayesian-differential-equations.html

@devmotion
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@devmotion
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@staticfloat It seems it's a problem specifically with aarch64 (or the workers) as it still works with x86_64: https://buildkite.com/julialang/turingtutorials/builds/78#b12d7990-0ba6-422b-9a30-df85278cc46d Probably bash does not support all features in the failing builds? The offending line seems to be https://github.com/staticfloat/coppermind-buildkite-plugin/blob/bc1c8b1f473651490bcaed15dfe16488d447a0e4/hooks/pre-command#L8.

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Ah no, it's just the exit code. So I assume bash might not be available and/or installed properly?

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Will be fixed by #298.

devmotion and others added 4 commits April 28, 2022 14:36
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

# This next command runs 3 independent chains without using multithreading.
# Sample 3 independent chains with forward-mode automatic differentiation (the default).
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Maybe add a link to the docs on how to change AD backends here?

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It's shown how to change it (and change it back) below, is that sufficiently clear? Or should we add a link here? Or maybe rather below?

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thanks for the clarification, that should be sufficient.

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There's one remaining issue, namely that pool_chain is not exported by MCMCChains. It's a hack anyway, so I think I'll just go and fix TuringLang/MCMCChains.jl#223. Then pool_chain is not needed anymore and the code becomes simpler.

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2 participants